Whaley was born in Pittsburgh, where he played high school football and went on to play at the collegiate level. He played college football at Pitt as a defensive back, collecting 4 interceptions during his tenure.
Whaley worked for the Steelers as a pro personnel coordinator. He worked there for 10 years before accepting the Buffalo Bills job. Whaley worked directly under Kevin Colbert the Director of Football Operations. In his time with the Steelers, Whaley helped scout and draft defensive players such as Lamarr Woodley, Troy Polamalu and Lawrence Timmons.
Whaley was named assistant general manager and Director of Pro Personnel of the Buffalo Bills on February 10, 2010. Whaley oversaw the team's Pro Personnel department and assisted General Manager Buddy Nix in all football-related administrative duties and in the college talent evaluation process until Nix stepped down from the general manager position on May 13, 2013. Whaley became Buffalo's GM three days later.
Whaley was, in conjunction with owners Terry and Kim Pegula and President Russ Brandon, responsible for the hiring of head coach Rex Ryan. After Ryan was relieved of his duties, the team announced that Whaley would lead the search for Ryan's successor.
On January 10, 2016, Whaley agreed to a contract extension offered to him by the Bills.
Whaley was "relieved of his duties" by the Bills on April 30, 2017.
Whaley gained unwanted notoriety in 2007, when an inappropriate e-mail that he had sent to Steelers assistant coach Larry Zierlein was inadvertently forwarded by Zierlein to a large number of high-level NFL employees, including commissioner Roger Goodell. Zierlein apologized for the gaffe, and it is believed that neither he nor Whaley was disciplined by the team or the league.
In a May 2016 radio interview, Whaley said of football: "It's a violent game that I personally don't think humans are supposed to play."
In December 2016, Whaley refused to explain his decision to bench the Bills' starting quarterback, Tyrod Taylor, prior to the last regular season game. Instead, interim head coach Anthony Lynn was forced to address questions from the media, and in an unscripted response, advised Taylor's benching was a 'business decision'. Whaley did not publicly comment on the decision.